Q'BIC Capstone Workshop 2011
Bioinformatics Component

• July 19: HW #3 is due Monday July 25. Bring hard copy to class.
• July 18: All project choices are due today by class time.
• July 18: HW #2 is due Tuesday July 19. Bring hard copy to class.
• July 18: Solutions to HW #1 can be found below.

• Summer Workshop

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Blackwell, Paperback, 2nd Edition, ISBN 978-0-470-08585-1
• [REFERENCE] Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• [REFERENCE] Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• [REFERENCE] Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.

• Homework #3: [html]; Due Monday Jul 25. Bring hard copy to class.
• PROJECT LIST: [pdf]
  • Pathogen Detection: Victoria, Rudolph, Claudia
  • Reverse Vaccinology: Egla, Jon, Patricia
  • RNA Folding: James, Diana
  • Riboswitches: Emmanuelle, Oscar
  • Horizontal Gene Transfer: Lorenzo, Natalie, Usman
• Homework #2: [html]; Due Tuesday July 19. Bring hard copy to class.
• Short Homework #1: Due Wednesday July 13, noon. Solutions [pdf]

• Jul 11: Lec 1[pdf] [Introduction & Biological preliminaries]; Reading: [Chapters 1, 2 (from JP); Extra]
• Jul 12: Lec 2[pdf] [BLAST, Global Sequence Alignment]; Reading: [Chapters 2, 3, 4 (from JP); Extra]
• Jul 13: Lec 3[pdf] [Local Sequence Alignment, Multiple Sequence Alignment, HMMs]; [Chapters 3, 4 (from JP)];
• Jul 14: Lec 4[pdf] [HMMs, Profile HMMs, Pattern Discovery];
• Jul 18: Lec 5[pdf] [Gene Expression, Microarray Technology];
• Jul 19: Lec 6[pdf] [Sequencing, Next Generation Sequencing, Applications of sequencing];
• Jul 20: Lec 7[pdf] [Multiple Hypothesis Testing; GO Annotations; Protein Structure];
• Jul 21: Lec 8[pdf] [Protein Structures; Machine Learning; Support Vector Machines];
• Jul 25: Lec 9[pdf] [Phylogenetics];

• Popular California Sea urchin genome sequenced, Nov 2006.
• Popular Time, Love, Memory, by Jonathan Weiner, 1999.